Iris Yellow Spot Virus Research Articles

A survey on the infection of Onion yellow dwarf virus and Iris yellow spot tospovirus in seed and bulb productions systems of onion in Calabria, Italy

A survey on the incidence of onion yellow dwarf virus (OYDV) and iris yellow spot virus (IYSV) was carried out over three production cycles of onion ‘Rossa di Tropea’ in Calabria, Italy. OYDV was found to be the prevalent virus. ‘Rossa di Tropea’ seedbeds adjacent to OYDV-infected green onion field had seedlings with 1.76% infection rate determining 36.2% and 98.67% infected plants in the bulbs and in the subsequent seed harvesting times, respectively. When seedbeds were at least one km away from other onion crops seedlings and bulb cultivation had the infection rate close to zero. OYDV was detected in whole plants except the roots and outer desiccated bulb skins. Seed transmission was not detected in ‘Rossa di Tropea’. Early OYDV infection significantly reduced the number and weight of seeds/inflorescence compared to late season infection, while the weight of 100 seeds was not different in the two early and late OYDV infected plants. IYSV was never found in seedbeds. It was always detected first in seed crops (April) than in bulb crops (June), and the final infection rate was higher in seed (2.67%–3.33%) than in bulb crops (0%–0.87%), suggesting there was an internal source of viral inoculum in the field. IYSV was detected in 3/123 apex bulbs randomly collected from stored bulbs and in 12/12 apex fresh bulbs collected at harvest time from infected plants, suggesting the role of bulbs as IYSV inoculum source. On the contrary, randomly collected bulbs (N = 109) from warehouse and bulbs of infected plants (N = 22), transplanted after storage, did not result in IYSV-infected plants.

English

Iris yellow spot virus (IYSV) is an important pathogen of Allium species worldwide. It has a tripartite genome consisting of the large (L), medium (M) and small (S) RNA segments. Despite its worldwide distribution, very few complete gene and genome sequences are available in public databases. The aim of this study was to obtain full gene sequences of a garlic-infecting IYSV isolate by next-generation sequencing (NGS) for understanding its evolution. Total RNA was extracted from an IYSV-positive garlic leaf and sequenced on the Illumina HiSeq platform using paired-end chemistry 125 × 125 bp reads. The quality of raw reads was assessed using FastQC software before trimming with Trimmomatic version 0.36. The resultant paired-end sequences were used for both de novo and reference-based genome assembly. The resultant consensus gene sequences were analyzed using SIAS (for sequence identity and composition), ExPASy (for protein molecular weight) and ORF Finder (for open reading frame identification). Three full gene sequences, that is, nucleocapsid (N), nonstructural protein (NSs) and movement protein (NSm) were recovered. The N gene did not display any distinct clustering patterns based on geographical locations and was most identical to an onion-infecting isolate from Serbia (Accession KT272878). The NSs and NSm genes clustered closely with homologous sequences of IYSV isolates that were retrieved from GenBank and EMBL. This study lays the foundation for complete genome studies of IYSV in Zimbabwe.   Key words: Allium species, emerging pathogen, reverse transcription polymerase chain reaction (RT-PCR), serology, tospovirus.

Iris yellow spot virus–induced chloroplast malformation results in male sterility

Iris yellow spot virus (IYSV) is one of the most devastating viral pathogens, which causes high economic losses in the onion yield. Physiological and genetic changes are associated with the appearance of chlorotic symptom in the infected plants. IYSV-N gene sequence analysis revealed that it shared sequence identity of 99% with other Egyptian isolates, at both genomic and proteomic levels. In addition, N protein sequence with computational examination indicated many motifs involved and played different roles in the virus activity and its regulation and stability were detected. In the Differential Display-Polymerase Chain Reaction (DD-PCR) study, a highly up-regulated gene at 15 days post-biological IYSV inoculation (dpi) was selected for sequencing. Based on the sequencing results that showed the identified gene was coding for a chloroplast-related gene, degenerate specific primers were designed for Real-Time PCR analysis. A significant change in the transcription level of the chloroplast-related gene after 15 dpi suggested that some IYSV proteins interact and/or regulate with chloroplast proteins and this finding supports the DD-PCR results. At 20 dpi, the ultrathin sections showed that IYSV infection caused many dramatic chloroplasts malformations. The malformation appeared as chloroplast broken envelope with the presence of numerous spherical particles inside it and chloroplasts with long stromule. Our findings indicated that IYSV interrupts normal chloroplast functions, as a part of the onion defence response, however many crucial factors remain to be elucidated and further studies are needed at both biological and molecular levels.

Tospoviruses (Family Bunyaviridae, Genus Tospovirus)

Viruses in the genus Tospovirus cause significant worldwide crop losses. The genus name is derived from the name of its first member, Tomato spotted wilt virus (TSWV). Initially observed in Australia in 1915, the spotted wilt disease of tomato was later shown to be of viral origin. The causal agent was designated TSWV, and considered to be the sole member of the tomato spotted wilt group of plant viruses until the early 1990s. At this time, the identification and characterization of several similar viruses, including Impatiens necrotic spot virus (INSV), led to the creation of the plant-infecting Tospovirus genus within the Bunyaviridae family, a large group of predominantly animal-infecting viruses. More than a dozen tospoviruses have since been identified and characterized and previously unknown species of the genus continue to be described on a regular basis. Three tospoviruses, TSWV, INSV and Iris yellow spot virus (IYSV), are known to occur in the US. This document is Fact Sheet PP-212, one of a series of the Plant Pathology Department, Florida Cooperative Extension Services, Institute of Food and Agricultural Sciences, University of Florida. Published October 2005.

Molecular identification, incidence and phylogenetic analysis of seven viruses infecting garlic in Ethiopia

Little information exists on the type and incidence of viruses infecting garlic (Allium sativum L) in Ethiopia. Attempts were made to identify the viruses using molecular techniques from 95 composite leaf samples collected from 44 farmers’ fields and 51 germplasm accessions. Reverse transcription (RT-) PCR using genus and/or virus specific primers was used to amplify partial genome sequences of potyviruses, allexiviruses, carlaviruses and a tospovirus followed by sequencing of PCR products. Results indicated that ~73.7% of the samples are infected with at least one virus. Onion yellow dwarf virus (OYDV, genus Potyvirus, family Potyviridae) is the most common virus detected followed by Garlic virus C (genus Allexivirus) and Shallot latent virus (SLV, genus Carlavirus). Other viruses detected at lower frequency include Garlic virus X and Garlic virus D (genus Allexivirus), Leek yellow stripe virus (genus Potyvirus) and Iris yellow spot virus (IYSV, genus Tospovirus). Mixed infection of two or more viruses was detected in 65.7% of the samples. Phylogenetic analysis suggested that the different viruses may have been introduced to Ethiopia from Europe or Asia. This is the first report of Garlic virus X, Garlic virus D, IYSV and SLV in garlic in Ethiopia. The high incidence of OYDV and IYSV which cause severe yield loss alone or in mixed infection with allexiviruses and carlaviruses is a cause of concern to growers.

Iris Yellow Spot Virus Prolongs the Adult Lifespan of Its Primary Vector, Onion Thrips (Thrips tabaci) (Thysanoptera: Thripidae).

Iris yellow spot virus (IYSV) from the genus Tospovirus, family Peribunyaviridae, reduces yield in several crops, especially Allium spp. IYSV is primarily transmitted by onion thrips (Thrips tabaci), but little is known about how IYSV impacts the biology of its principal vector. In a controlled experiment, the effect of IYSV on the lifespan and fecundity of onion thrips was examined. Larvae were reared on IYSV-infected onions until pupation. Individual pupae were confined until adults eclosed, and the lifespan and total progeny produced per adult were monitored daily. Thrips were tested for the virus in reverse-transcriptase polymerase chain reaction using specific primers to confirm the presence of IYSV. Results indicated that 114 and 35 out of 149 eclosing adults tested positive (viruliferous) and negative (nonviruliferous) for IYSV, respectively. The viruliferous adults lived 1.1–6.1 d longer (average of 3.6 d) than nonviruliferous adults. Fecundity of viruliferous and nonviruliferous onion thrips was similar with 2.0 ± 0.1 and 2.3 ± 0.3 offspring produced per female per day, respectively. Fecundity for both viruliferous and nonviruliferous thrips also was significantly positively correlated with lifespan. These findings suggest that the longer lifespan of viruliferous onion thrips adults may allow this primary vector of IYSV to infect more plants, thereby exacerbating IYSV epidemics.

Improved Tolerance for Onion Thrips and Iris Yellow Spot in Onion Plant Introductions after Two Selection Cycles

Iris yellow spot (IYS), a disease caused by Iris yellow spot virus (IYSV) and spread by onion thrips, is a devastating disease of onion bulb and seed production. The development of onion germplasm resistant to IYS and/or thrips is crucial to onion production, since host plant resistance is unknown for both pests. During the summer of 2010 and 2012, plants with fewer IYS disease symptoms were selected from a screening of plant introduction accessions (PIs) and first-generation selections, respectively. The resulting progeny from these selected plants were evaluated during the summers of 2013 and 2014 for thrips numbers and IYS symptom expression, and compared with their respective original PIs and a susceptible check, ‘Rumba’. The field experiment was designed such that every plant in the field screening had an equal chance of being infected with IYSV. This study shows that variation for thrips and IYS existed among PIs and first- and second-generation selections. Even though not enough progress towards minimizing IYS severity was evident from this study, we did identify several lines with improved tolerance to onion thrips in first- and second-generation selections. The majority of the selected lines exhibited lower thrips and IYS severity compared to ‘Rumba’, which suggests that the progress towards developing insect- and ultimately disease-resistant germplasm can be achieved.

Endophytic Colonization of Onions Induces Resistance Against Viruliferous Thrips and Virus Replication.

In agricultural ecosystems, insect pests, pathogens, weather patterns, and reduced soil fertility pose major challenges to crop productivity and are responsible for significant yield losses worldwide. Iris yellow spot virus (IYSV) vectored by Thrips tabaci Lindeman, is a major hindrance to onion production in eastern Africa. Control measures often rely on insecticides with deleterious effects. Endophytes are one key alternative as they can play important roles in mediating induced systemic resistance. Hence, we examined the potential effect of endophytic fungus Hypocrea lixii (F3ST1) on feeding and replication of IYSV on endophyte-colonized (E+) and endophyte-free (E-) onion plants. For more precise assessment, replication was also tested using leaf disk bioassays and individual thrips. The number of feeding punctures was significantly lower in E+ as compared to E- plants. Disease level was significantly lower in E+ as compared to E- plants for four weeks post-exposure to thrips. IYSV replication was reduced by 2.5-fold in endophytic treatment on both whole plant and leaf disk assays. Thrips tabaci showed 2 times higher feeding activities on endophyte-free onion leaf disks as compared to the endophyte-inoculated leaf disks. Our results suggest potential utility of the endophytes to reduce feeding damage and virus infection on onion plants. Further studies should be conducted to elucidate the secondary metabolites involved in such endophyte-thrips-virus mediated interaction and determine whether the interactions extend for this and other onion varieties and viruses under field conditions.

Identification of genes differentially expressed in onion infected with Iris yellow spot virus

Iris yellow spot virus (IYSV) causes severe damage and economic losses in onion production. Differential display-PCR was used to study changes in the gene expression of IYSV-infected onion plants. Representative up-regulated and down-regulated genes were selected for further study. Based on sequence analysis, the up-regulated genes were identified as retrotransposon protein, disease resistance-like proteins, chitinase, pathogenesis-related protein, cytochrome oxidase, cytochrome c, pentatricopeptide repeat-containing protein and pectin methylesterase. A DNA-binding transcriptional repressor protein gene was greatly down-regulated. . Most of the identified genes are known to play essential roles in plant defence systems, and are newly identified in onion sequences.

Seasonal dynamics and alternate hosts of thrips transmitted Iris yellow spot virus in Kenya

Thrips-transmitted Iris yellow spot virus (IYSV) (Family Tospoviridae, Genus Orthotospovirus) is a major constraint to onion (Allium cepa L.) production in Kenya. Determining seasonal patterns of the vector and alternate hosts of the virus could help onion farmers plan Integrated Pest Management strategies; while allowing them to move away from calendar-based applications of insecticides. The objective of this study was to determine the distribution, seasonal variations and alternate hosts of vector and IYSV. For distribution, a survey was carried out on a network of farms in all onion growing areas in Kenya; while for seasonality, surveys were done in two areas; Loitoktok and Naivasha. Data were collected on IYSV incidence, thrips population and alternate hosts. Results showed IYSV was widely distributed in all onion growing areas; with incidence varying from 26 to 72%. Highest IYSV incidence was recorded during the cool-dry season, and varied from 56.5 to 71%; while lowest IYSV incidence in onions was observed during the cool and wet season (29.9 to 32.2%). Iris yellow spot disease incidence positively correlated with the number of onion thrips in Loitokitok (r = 0.659; P<0.0001) and Naivasha (r = 0.623; P<0.0001). Identified alternate hosts for IYSV were leeks, chives, shallots, lambsquarters, redroot pigweed, Chinese lantern and black nightshade.Occurrence of thrips on onions, which is grown all year round calls for urgent integrated pest management strategies that includes host plant resistance, field sanitation, forecasting and use of beneficial insects and parasitoids to reduce impact of the pest and disease. Plant health adherence through removal of alternate weeds hosts around the cultivated fields, would be useful in minimising IYSV incidence.Keywords: Allium cepa, chives, lambsquarters, leeks, shallots, tospoviruses

Selection Progress for Resistance to Iris Yellow Spot in Onions

Onion thrips (Thrips tabaci Lindeman)–vectored Iris yellow spot virus (IYSV) causes the disease Iris yellow spot (IYS), which is a major threat to the sustainability of onion production worldwide. An increase in thrips resistance to various insecticides, high costs, and the limited efficacy of insecticides under hot and drier conditions found in various onion-growing regions restrict grower’s options for effective control of thrips and spread of IYSV. Because cultivars resistant to thrips and IYS are lacking, this study was undertaken to measure selection progress for IYS resistance after one selection cycle. In 2009, selections were performed on previously evaluated New Mexico State University (NMSU) breeding lines that showed some reduced IYS disease symptoms, and the selected plants self-pollinated the following year. In 2011 and 2012, plants from the original and selected populations along with a susceptible check, ‘Rumba’, were evaluated under field conditions when onion thrips and IYSV were present. Plants were rated for IYS disease severity and the number of thrips per plant was recorded three times during the study in each year. First-generation material, NMSU 10-776, NMSU 10-782, NMSU 10-785, NMSU 10-807, and NMSU 10-813, had fewer thrips number per plant, lower disease severity, and disease incidence than their original breeding lines on at least one or two rating times in both years. Some first-generation breeding lines performed better with a lower thrips number and disease severity than their original population in 1 year or the other. Most entries exhibited fewer thrips, lower IYS disease severity, and less incidence than the susceptible check ‘Rumba’ at most rating times. Overall, some progress was observed in this first-generation material for reduced IYS disease symptom expression when compared with their original populations.

First Report of Iris yellow spot virus Infecting Garlic in Pakistan.

First Report of Iris yellow spot virus Infecting Garlic in Pakistan.

Potential factors contributing to the decline of Iris Yellow Spot Virus in organically grown onion crops in Canterbury and Hawke's Bay over three years

The Tospovirus Iris yellow spot virus (IYSV), transmitted by thrips (predominantly Thrips tabaci), was first recorded in New Zealand in 2007. In March 2015, symptoms of the virus were relatively widespread in an organically managed onion crop in Canterbury. Onion plants were sampled for the presence of T. tabaci adults and larvae and for IYSV symptoms on an organically managed farm in Canterbury in 2014-2015, 2015-16 and 2016-17, and on a similar farm in Hawke's Bay in 2014-2015 and 2015-16. An immunoassay was used to confirm the presence of IYSV in some symptomatic plants. In Canterbury, IYSV symptoms were less apparent in 2015-16 and no symptoms were observed in 2016-17. No IYSV symptoms were observed in the Hawke's Bay onion crop, despite relatively high T. tabaci numbers. The virus symptoms declined from when they were first observed in March 2015 to undetectable levels in 2016-17 in Canterbury, which may be attributed to crop location, fewer thrips and the absence of a disease reservoir in volunteer Allium cepa plants or other hosts.

Development of a sensitive Luminex xMAP-based microsphere immunoassay for specific detection of Iris yellow spot virus

BackgroundIris yellow spot virus (IYSV) is an Orthotospovirus that infects most Allium species. Very few approaches for specific detection of IYSV from infected plants are available to date. We report the development of a high-sensitive Luminex xMAP-based microsphere immunoassay (MIA) for specific detection of IYSV.ResultsThe nucleocapsid (N) gene of IYSV was cloned and expressed in Escherichia coli to produce the His-tagged recombinant N protein. A panel of monoclonal antibodies (MAbs) against IYSV was generated by immunizing the mice with recombinant N protein. Five specific MAbs (16D9, 11C6, 7F4, 12C10, and 14H12) were identified and used for developing the Luminex xMAP-based MIA systems along with a polyclonal antibody against IYSV. Comparative analyses of their sensitivity and specificity in detecting IYSV from infected tobacco leaves identified 7F4 as the best-performed MAb in MIA. We then optimized the working conditions of Luminex xMAP-based MIA in specific detection of IYSV from infected tobacco leaves by using appropriate blocking buffer and proper concentration of biotin-labeled antibodies as well as the suitable ratio between the antibodies and the streptavidin R-phycoerythrin (SA-RPE). Under the optimized conditions the Luminex xMAP-based MIA was able to specifically detect IYSV with much higher sensitivity than conventional enzyme-linked immunosorbent assay (ELISA). Importantly, the Luminex xMAP-based MIA is time-saving and the whole procedure could be completed within 2.5 h.ConclusionsWe generated five specific MAbs against IYSV and developed the Luminex xMAP-based MIA method for specific detection of IYSV in plants. This assay provides a sensitive, high-specific, easy to perform and likely cost-effective approach for IYSV detection from infected plants, implicating potential broad usefulness of MIA in plant virus diagnosis.

Survey of viruses infecting garlic in Samsun, Turkey

Garlic is one of the most important Allium crops in Turkey. A survey for viruses infecting garlic (Allium sativum L.) was carried out in Samsun, Turkey. A total of seventy samples were collected and checked by biological and serological methods for the presence of Onion yellow dwarf virus (OYDV), Leek yellow stripe virus (LYSV), Garlic common latent virus (GarCLV), Shallot latent virus (SLV), and Iris yellow spot virus (IYSV) using virus-specific antiserum. OYDV was detected by double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA) and bioassay in garlic (5.7%) samples collected from Samsun, Turkey.

Importance of Transplanted Onions Contributing to Late-Season Iris yellow spot virus Epidemics in New York.

Iris yellow spot virus (IYSV) is an economically significant tospovirus of onion transmitted by onion thrips (Thrips tabaci Lindeman). IYSV epidemics in onion fields are common in New York; however, the role of various habitats contributing to viruliferous onion thrips populations and IYSV epidemics is not known. In a 2-year field study in New York, the abundance of dispersing onion thrips, including those determined to be viruliferous via reverse-transcriptase polymerase chain reaction, was recorded in habitats known to harbor both IYSV and its vector. Results showed that viruliferous thrips were encountered in all habitats; however, transplanted onion sites accounted for 49 to 51% of the total estimated numbers of viruliferous thrips. During early to midseason, transplanted onion sites had 9 to 11 times more viruliferous thrips than the other habitats. These results indicate that transplanted onion fields are the most important habitat for generating IYSV epidemics in all onion fields (transplanted and direct-seeded) in New York. Our findings suggest that onion growers should control onion thrips in transplanted fields early in the season to minimize risk of IYSV epidemics later in the season.

Variabilidad y síntomas causados por Iris yellow spot virus en Nicotiana benthamiana

<p>En cultivos de cebolla <em>Allium cepa</em> del estado de Morelos, México, se observan síntomas típicos y severos asociados a <em>Iris yellow spot virus </em>(IYSV). En esta investigación se estudiaron las alteraciones que ocasionan los aislamientos de IYSV procedentes de síntomas típicos y severos en <em>Nicotiana benthamiana</em>, las diferencias en el gen N y su filogenia. Cuatro aislamientos típicos y cinco severos inoculados mecánicamente causaron infección sistémica. En cámara bioclimática los aislamientos severos ocasionaron mayor severidad de síntomas. La secuencia del gen N de ambos aislamientos tuvo 98-99% de identidad con la nucleoproteína de IYSV y no se observaron cambios en la secuencia de nucleótidos entre ellos. Ambos aislamientos se agruparon con el genotipo IYSV<sub>BR</sub> y tuvieron mayor similitud con los reportados en Canadá y Estados Unidos.</p>

Evaluating integrated pest management tactics for onion thrips and pathogens they transmit to onion

Onion thrips (Thrips tabaci) is a significant pest of onion worldwide, causing both direct and indirect damage to the crop. Integrated pest management of onion thrips should improve profitability and sustainability of onion production. Promising management approaches include reducing nitrogen application rates, using thrips-resistant cultivars and implementing action threshold-based insecticide programs. However, the impact of these integrated pest management approaches on thrips densities and damage, crop yield, and thrips-associated plant diseases like iris yellow spot (IYS) (caused by Iris yellow spot virus) and bacterial center rot (caused by Pantoea agglomerans and P. ananatis) remains largely unknown. In a two-year field trial in New York, combinations of varying levels of nitrogen applied at planting (67, 101 and 140kgha−1) and different insecticide programs (standard weekly insecticide program and action threshold-based insecticide program) were evaluated for onion thrips management in onion cultivars that had moderate resistance (‘Avalon’), low resistance (‘Delgado’) and no resistance (‘Bradley’) to onion thrips. Results indicated that regardless of cultivar, nitrogen did not affect larval thrips densities, onion yields, IYS or bacterial center rot. Across all cultivars, insecticide use (both programs) significantly reduced larval thrips densities and damage, IYS severity and incidence, and increased onion yield. Insecticide use did not consistently affect the incidence of bacterial center rot. Both insecticide programs reduced onion thrips larval densities by 60–81% relative to the untreated control, but the action threshold-based application program used 2.8 fewer applications than the standard program. ‘Avalon’ had low thrips densities and IYS disease, but required the same number of insecticide applications as ‘Bradley’. Onion yields in both insecticide programs were statistically similar in both years, and bulb weights averaged 10–54% more than those in the untreated control. Our results indicated that growers can reduce nitrogen levels at planting and insecticide use without compromising control of either onion thrips or IYS disease or onion bulb yields.

First report of Iris yellow spot virus in Costa Rica

Iris yellow spot virus (IYSV), an emerging disease of onion crops, was identified by transmission electron microscopy, enzyme linked immunosorbent assay, and reverse transcription polymerase chain reaction in Costa Rica. Onion plants had straw-colored, elongated lesions and tip dieback. Costa Rican IYSV nucleocapsid partial sequences (15 isolates) grouped with isolates from North and Central America and from New Zealand.

Evaluating Iris Yellow Spot Disease Incidence and Severity in Onion Germplasm of Varying Leaf Characteristics

Iris yellow spot (IYS) disease, caused by Iris yellow spot virus (IYSV), results in irregular and diamond-shaped, chlorotic, and necrotic lesions on the leaves and seedstalks of onions (Allium cepa L.). These lesions reduce leaf photosynthetic area and ultimately reduce onion bulb size and yield from larger bulb classes. IYSV is vectored by onion thrips (Thrips tabaci L.) that are difficult to control under certain environmental conditions. Currently, no onion cultivar is resistant to the disease symptoms, virus, and/or thrips. Twenty-one cultivars and 17 germplasm lines were evaluated in the field for IYS disease severity and thrips densities at multiple times during the season as well as leaf color, waxiness, and axil openness of these entries. Plants were grown under conditions that favored thrips populations (high temperatures, low moisture, and no insecticidal spray applications), IYSV presence and distribution, and IYS development. Plants of New Mexico State University (NMSU) 07-10-1 had fewer thrips than several entries later in the season in both 2009 and 2010. Several entries exhibited a lower number of thrips per plant early or later in the season; however, these results were not consistent across years and were not associated with a particular foliage characteristic. Lighter leaf color and/or a lesser amount of epicuticular wax did not always result in the fewest number of thrips per plant as has been reported in the literature. Plants of NMSU 09-58 tended to exhibit fewer and less severe IYS symptoms early in the season as compared with plants of other entries.